Nasopharyngeal colonization with pathobionts is associated with susceptibility to respiratory illnesses in young children

Abstract

Some children are more susceptible to viral and bacterial respiratory infections in the first few years of life than others. However, the factors contributing to this susceptibility are incompletely understood. In a retrospective analysis of clinical samples collected from a prospectively-enrolled cohort of 358 children we sought associations between physician-attended illness visits and bacterial colonization in the first five years of life. A subset of children was identified by unsupervised clustering analysis as infection and allergy prone (IAP). Several respiratory infection- and allergy-mediated illnesses co-occurred at higher rates in IAP children, while the rates of other illnesses were not significantly different between the groups. Analyses of nasopharyngeal (NP) pathobionts and microbiota commensals showed that early age of first colonization with pathobionts Streptococcus pneumonia, non-typeable Haemophilus influenzae, and Moraxella catarrhalis was associated with IAP children, and particularly Moraxella abundance was negatively associated with NP microbiome diversity. We conclude that mucosal pathobiont exposures in early life can influence susceptibility to respiratory illnesses in children.

Fig 1. Identification of infection and allergy-prone (IAP) children.

A) Identified clusters from cohort of 358 children based on physician diagnosis of illnesses from 6 to 60 months of age. Contours show the density of subjects independent of assigned IAP status. B) Comparison of overall physician-attended illness visits from 6 to 30 months of age in IAP (red, n = 99) and NIAP (blue, n = 259) children. *: p value <0.05 by Wilcox test.

Fig 2. Comparison of individual conditions in IAP and NIAP children.

Physician diagnosis of various respiratory (A) and non-respiratory (B) conditions were compared between IAP and NIAP children. *: p value <0.05 by chi square test comparing proportions.

Fig 3. Pathobiont colonization in IAP and NIAP children.

A) The age at first colonization with S. pneumoniae, H. influenzae and/or M. catarrhalis as microbiologically identified in child NP samples from 6 to 40 months of age are shown (n = 98 IAP, 256 NIAP). The proportion of colonization-negative children throughout the time course are represented as the surviving cohort in the analysis. B) Age at first colonization with combinations of pathobionts as shown. p values from log-rank test are displayed on each graph.

Fig 4. Nasopharyngeal 16S rRNA analysis at 6 months of age.

A) Genera found to be differently abundant between IAP and NIAP groups by pairwise Wilcox with Holm-Bonferroni adjustment. B) Shannon diversity of NP microbiome in IAP and NIAP children at 6 months of age. p value for Wilcox test is shown. C) Average frequency of each genus in IAP and NIAP children. D) Correlation analysis of individual genus frequency and Shannon diversity for each child. Shown are all genera that were significantly correlated (p<0.05) using a linear model expressing Shannon diversity as a function of each bacterial genus and IAP status. n = 14 IAP and 20 NIAP samples analyzed.